If anyone's interested, there is actually a way to repair permissions even with SIP disabled. So FYI:
https://www.firewolf.science/2015/07/repairpermissions-v2-0-cli/
This saved me a lot of hassle reinstalling the whole system, thanks to "Firewolf"!
However, there are probably only a few rare cases where repairing permissions is actually required now.
Before Kurt Jung's excellent article on font management was updated (
http://www.jklstudios.com/misc/osxfonts.html#requiredfonts), I moved some system/library/fonts and had to reinstall them. The permissions for those fonts got messed up. I strongly recommend you read that font management article carefully to avoid mistakes similar to mine. Many fonts you would not expect are tied into the system's interface. I suspect that merely deleting fonts won't mess up the permissions, but reinstalling them does.
Access the El Cap recovery partition (Command + r keys at boot) and disable SIP (Utilities Menu, Terminal: "csrutil disable" command, reboot) Once you visit Firewolf's web site, scroll down, find the link, and download the new KCMP Utility Pro version 3.0. Use it to install the RepairPermissions utility. You have to have SIP disabled and reboot into single user mode (Command + R keys) to use the RepairPermissions utility on the startup volume.
In my case the utility found and fixed several errors with, you guessed it, only the fonts I had errantly reinstalled. No other errors were found.